Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Phymateus saxosus (Coquerel, 1861) (Orthoptera: Pyrgomorphidae) and phylogenetic analysis.

ABSTRACT: Phymateus saxosus is a member of the family Pyrgomorphidae, Orthoptera. In this study, the complete mitochondrial genome (mitogenome) of P. saxosus was determined and analyzed. Assembled mitogenome sequence of P. saxosus is 15,672 bp in size, containing 37 genes and a control region. The gene orientation and arrangement of P. saxosus are identical to other species in the Pyrgomorphoidea family. The overall nucleotide composition is as follows: A (43.6%) > T (30.2%) > C (16.1%) > G (10.1%). Phylogenetic analysis suggested that P. saxosus forms sister groups with P. morbillosus, and the monophyly of Pyrgomorphidae is supported. In general, this study provided valuable genetic information for P. saxosus and explored the phylogenetic relationships in the family Pyrgomorphidae.

SUBMITTER: Chang H

PROVIDER: S-EPMC11000610 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of Phymateus saxosus (Coquerel, 1861) (Orthoptera: Pyrgomorphidae) and phylogenetic analysis.

Chang Huihui H Liu Xinhu X Xie Zhaohui Z

Mitochondrial DNA. Part B, Resources 20240404 4

Phymateus saxosus is a member of the family Pyrgomorphidae, Orthoptera. In this study, the complete mitochondrial genome (mitogenome) of P. saxosus was determined and analyzed. Assembled mitogenome sequence of P. saxosus is 15,672 bp in size, containing 37 genes and a control region. The gene orientation and arrangement of P. saxosus are identical to other species in the Pyrgomorphoidea family. The overall nucleotide composition is as follows: A (43.6%) > T (30.2%) > ...[more]

PMID: 38591051

Similar Datasets

Complete mitochondrial genome of giant cricket Tarbinskiellus portentosus (Orthoptera: Gryllinae) and phylogenetic analysis.

Project description:Tarbinskiellus portentosus (Lichtenstein, 1796) is an agricultural and forestry pest, but people in some places use it as a delicacy. The complete mitogenome of T. portentosus (GenBank accession number MZ427921) is 15, 498 bp in size, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a noncoding A + T-rich region. The A + T-rich region is located between 12S rRNA and tRNAIle . The base composition of the whole T. portentosus mitogenome is 40.62% for A, 9.87% for G, 32.20% for T, and 17.31% for C, with a high AT content of 72.82%. The phylogeny analysis indicated that T. portentosus had a close relationship with Cardiodactylus muiri. The present data could contribute to further detailed diversity and phylogeographic analysis for this edible cricket.

| S-EPMC8820803 | biostudies-literature

Complete mitochondrial genome of the branching octocoral Paramuricea grayi (Johnson, 1861), phylogenetic relationships and divergence analysis.

Project description:The Gray's sea fan, Paramuricea grayi (Johnson, 1861), typically inhabits deep littoral and circalittoral habitats of the eastern temperate and tropical Atlantic Ocean. Along the Iberian Peninsula, where P. grayi is a dominant constituent of circalittoral coral gardens, two segregating lineages (yellow and purple morphotypes) were recently identified using single-copy nuclear orthologues. The mitochondrial genomes of 9 P. grayi individuals covering both color morphotypes were assembled from RNA-seq data, using samples collected at three sites in southern (Sagres and Tavira) and western (Cape Espichel) Portugal. The complete circular mitogenome is 18,668 bp in length, has an A + T-rich base composition (62.5%) and contains the 17 genes typically found in Octocorallia: 14 protein-coding genes (atp6, atp8, cob, cox1-3, mt-mutS, nad1-6, and nad4L), the small and large subunit rRNAs (rns and rnl), and one transfer RNA (trnM). The mitogenomes were nearly identical for all specimens, though we identified a noteworthy polymorphism (two SNPs 9 bp apart) in the mt-mutS of one purple individual that is shared with the sister species P. clavata. The mitogenomes of the two species have a pairwise sequence identity of 99.0%, with nad6 and mt-mutS having the highest rates of non-synonymous substitutions.

| S-EPMC9673786 | biostudies-literature

Complete Mitochondrial Genome Sequence of Acrida cinerea (Acrididae: Orthoptera) and Comparative Analysis of Mitochondrial Genomes in Orthoptera.

Project description:The complete 15,599-bp mitogenome of Acrida cinerea was determined and compared with that of the other 20 orthopterans. It displays characteristic gene content, genome organization, nucleotide composition, and codon usage found in other Caelifera mitogenomes. Comparison of 21 orthopteran sequences revealed that the tRNAs encoded by the H-strand appear more conserved than those by the L-stand. All tRNAs form the typical clover-leaf structure except trnS (agn), and most of the size variation among tRNAs stemmed from the length variation in the arm and loop of TΨC and the loop of DHU. The derived secondary structure models of the rrnS and rrnL from 21 orthoptera species closely resemble those from other insects on CRW except a considerably enlarged loop of helix 1399 of rrnS in Caelifera, which is a potentially autapomorphy of Caelifera. In the A+T-rich region, tandem repeats are not only conserved in the closely related mitogenome but also share some conserved motifs in the same subfamily. A stem-loop structure, 16 bp or longer, is likely to be involved in replication initiation in Caelifera and Grylloidea. A long T-stretch (>17 bp) with conserved stem-loop structure next to rrnS on the H-strand, bounded by a purine at either end, exists in the three species from Tettigoniidae.

| S-EPMC3004375 | biostudies-literature

The complete mitochondrial genome of Sinopodisma hengshanica (Orthoptera: Acrididae) and its phylogenetic implication.

Project description:The complete mitochondrial genome (mitogenome) of Sinopodisma hengshanica (Orthoptera: Acrididae) was firstly determined and analyzed in the present study. Assembled mitogenome sequence of S. hengshanica is 15,623 bp in size, containing 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), as well as one A + T-rich region. Its gene component and arrangement are identical with other Acrididae species. The overall nucleotide composition is as follows: A (42.89%), G (10.34%), T (33.07%), and C (13.70%). All PCGs are initiated by typical ATN codons, and terminated with harboring complete stop codons TAA and TAG. Furthermore, phylogenetic trees were reconstructed based on 13 PCGs to validate the taxonomic status of S. hengshanica, exhibiting a close relationship with Sinopodisma rostellocerca.

| S-EPMC8986288 | biostudies-literature

Characterization of the complete mitochondrial genome of Ergatettix serrifemora (Orthoptera: Tetrigidae) from China and its phylogenetic analysis.

Project description:The mitochondrial genome (mitogenome) of the Ergatettix serrifemora (Orthoptera: Tetrigidae: Tetriginae) was sequenced and annotated. The assembled mitochondrial genome was 14,947 bp, containing 45.8% of A, 15.7% of C, 9.6% of G and 28.9% of T, respectively, which is the classical structure for insect mitogenome. The region that we failed to sequence was between rrnS and trnI, and generally contained a putative AT-rich region. Twelve PCGs started with typical ATN codon and eleven ended with complete stop codons (three with TAG, eight with TAA). The phylogenetic trees in the current study confirmed that E. serrifemora was clustered with other Tetriginae species, and this study would improve our understanding for the mitogenomes of Tetrigoidea.

| S-EPMC7782885 | biostudies-literature

The complete mitochondrial genome of Xizicus (Haploxizicus) maculatus revealed by Next-Generation Sequencing and phylogenetic implication (Orthoptera, Meconematinae).

Project description:Xizicus Gorochov, 1993, the quiet-calling katydid, is a diverse genus with 68 species in world, which includes more than 45 species in China, has undergone numerous taxonomic revisions with contradicting conclusions. In this study the complete mitochondrial genome of Xizicus (Haploxizicus) maculatus collected from Hainan for the first time was sequenced using the Next-Generation Sequencing (NGS) technology. The length of whole mitogenome is 16,358 bp and contains the typical gene arrangement, base composition, and codon usage found in other related species. The overall base composition of the mitochondrial genome is 37.0 % A, 32.2 % T, 20.2 % C, and 10.6 % G. All 13 protein-coding genes (PCGs) began with typical ATN initiation codon. Nine of the 13 PCGs have a complete termination codon, but the remaining four genes (COI, COIII, ND5, and ND4) terminate with an incomplete T. Phylogenetic analyses are carried out based on the concatenated dataset of 13 PCGs and two rRNAs of Tettigoniidae species available in GenBank. Both Bayesian inference and Maximum Likelihood analyses recovered each subfamily as a monophyletic group. Regardless of the position of Lipotactinae, the relationships among the subfamilies of Tettigoniidae were as follows: ((((Tettigoniinae, Bradyporinae) Meconematinae) Conocephalinae) Hexacentrinae). The topological structure of the phylogeny trees showed that the Xizicus (Haploxizicus) maculatus is closer to Xizicus (Xizicus) fascipes than Xizicus (Eoxizicus) howardi.

| S-EPMC6048180 | biostudies-literature

First record of mitochondrial genome of Teredorus nigropennis (Orthoptera: Tetrigidae) and phylogenetic analysis.

Project description:The nearly complete mitochondrial genome (mitogenome) of Teredorus nigropennis was determined and analyzed. This mitogenome was 14,652 bp in size and encoded 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes. The most common start codon is ATN, the most common termination codon is TAA and two genes have incomplete termination codon T (TA). The overall nucleotide composition was 45.2% of A, 10.2% of G, 28.6% of T, and 16.1% of C. The data will increase the basic information of Tetrigidae phylogenetic research and can help to better understand the phylogenetic status of T. nigropennis in Tetrigiodea.

| S-EPMC7510836 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Rubus sumatranus Miq 1861 (Roseaceae).

Project description:The wild raspberry species Rubus sumatranus Miq 1861 is a promising resource for breeding thermotolerant cultivars. Its complete chloroplast genome spans 155,935 base pairs (bp), featuring the classic quadripartite structure: an 18,729 bp small single-copy region, an 85,662 bp large single-copy region, and two 25,772 bp inverted repeats. A total of 130 genes were identified, including 86 protein-coding, 36 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogenetic tree based on chloroplast genomes shows that R. sumatranus, within the subgenus Idaeobatus, is sister to the subgenus Batothamnus. This confirms the polyphyletic nature of the subgenus Idaeobatus. The chloroplast genome assembly of R. sumatranus enhances our understanding of its evolutionary history.

| S-EPMC11626868 | biostudies-literature

The complete mitochondrial genome of Fruhstorferiola tonkinensis (Orthoptera: Catantopidae).

Project description:Fruhstorferiola tonkinensis belongs to the group of Catantopidae, which is the largest group in Acridoidae. The complete mitochondrial genome (mitogenome) of Fruhstorferiola tonkinensis is 15,637 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes and 1 A + T-rich region. The gene order and arrangement are identical to other Acridoidae species. Most PCGs (except for the ATP6) start with the typical ATN codons, while most stop codons are TAA, TAG. The combined dataset of 13 PCGs and 2 rRNAs from 17 grasshoppers (including 15 Catantopidae species and 2 outgroups) is used to construct phylogenetic tree and analyse phylogenetic relationship of Catantopidae.

| S-EPMC7800193 | biostudies-literature

The complete mitochondrial genome of Fruhstorferiola huayinensis (Orthoptera: Catantopidae).

Project description:The complete mitochondrial genome of Fruhstorferiola huayinensis is 16 227 bp in length, and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region. In control region, a tRNAIle-like sequence was identified. Additionally, a 259 bp long tandem repeat was identified in the control region. Using the 13 PCGs and 2 rRNA of F. huayinensis, together with 14 other close-related and 2 outgroup species, we constructed BI phylogenetic tree to verify the accuracy and utility of new determined mitogenome sequences.

| S-EPMC7871826 | biostudies-literature